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Yorodumi- EMDB-8354: Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8354 | |||||||||
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Title | Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703 | |||||||||
Map data | B-factor sharpened, masked map generated from relion auto-refinement and postprocessing | |||||||||
Sample |
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Function / homology | Function and homology information detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / calcium-induced calcium release activity / regulation of calcium ion import / cation channel complex / muscle alpha-actinin binding / placenta blood vessel development / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / voltage-gated monoatomic cation channel activity / cellular response to fluid shear stress / cellular response to osmotic stress / non-motile cilium / outward rectifier potassium channel activity / actinin binding / motile cilium / transcription regulator inhibitor activity / aorta development / determination of left/right symmetry / inorganic cation transmembrane transport / neural tube development / protein heterotetramerization / ciliary membrane / voltage-gated sodium channel activity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / voltage-gated potassium channel activity / potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / cell surface receptor signaling pathway via JAK-STAT / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / embryonic placenta development / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / potassium ion transmembrane transport / cytoskeletal protein binding / cellular response to calcium ion / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / phosphoprotein binding / protein tetramerization / cytoplasmic vesicle membrane / mitotic spindle / Wnt signaling pathway / cilium / cellular response to reactive oxygen species / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / heart development / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / ATPase binding / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Shen PS / Yang X / DeCaen PG / Liu X / Bulkley D / Clapham DE / Cao E | |||||||||
Citation | Journal: Cell / Year: 2016 Title: The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs. Authors: Peter S Shen / Xiaoyong Yang / Paul G DeCaen / Xiaowen Liu / David Bulkley / David E Clapham / Erhu Cao / Abstract: The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM ...The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM structure of PKD2 in lipid bilayers at 3.0 Å resolution, which establishes PKD2 as a homotetrameric ion channel and provides insight into potential mechanisms for its activation. The PKD2 voltage-sensor domain retains two of four gating charges commonly found in those of voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter and near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction. The extracellular domain of PKD2, a hotspot for ADPKD pathogenic mutations, contributes to channel assembly and strategically interacts with the transmembrane core, likely serving as a physical substrate for extracellular stimuli to allosterically gate the channel. Finally, our structure establishes the molecular basis for the majority of pathogenic mutations in Pkd2-related ADPKD. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8354.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-8354-v30.xml emd-8354.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8354_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_8354_1.png emd_8354_2.png | 178 KB 244.4 KB | ||
Masks | emd_8354_msk_1.map | 27 MB | Mask map | |
Others | emd_8354_half_map_1.map.gz emd_8354_half_map_2.map.gz | 17.9 MB 17.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8354 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8354 | HTTPS FTP |
-Validation report
Summary document | emd_8354_validation.pdf.gz | 632.4 KB | Display | EMDB validaton report |
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Full document | emd_8354_full_validation.pdf.gz | 632 KB | Display | |
Data in XML | emd_8354_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_8354_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8354 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8354 | HTTPS FTP |
-Related structure data
Related structure data | 5t4dMC 8355C 8356C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8354.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | B-factor sharpened, masked map generated from relion auto-refinement and postprocessing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8354_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: RELION half map 2 (relion refine)
File | emd_8354_half_map_1.map | ||||||||||||
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Annotation | RELION half map 2 (relion_refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION half map 1 (relion refine)
File | emd_8354_half_map_2.map | ||||||||||||
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Annotation | RELION half map 1 (relion_refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hPKD:198-703
Entire | Name: hPKD:198-703 |
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Components |
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-Supramolecule #1: hPKD:198-703
Supramolecule | Name: hPKD:198-703 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI-/- / Recombinant plasmid: pFastbac1 |
-Macromolecule #1: hPKD:198-703, Polycystin-2
Macromolecule | Name: hPKD:198-703, Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 59.429145 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GAMGSRGLWG TRLMEESSTN REKYLKSVLR ELVTYLLFLI VLCILTYGMM SSNVYYYTRM MSQLFLDTPV SKTEKTNFKT LSSMEDFWK FTEGSLLDGL YWKMQPSNQT EADNRSFIFY ENLLLGVPRI RQLRVRNGSC SIPQDLRDEI KECYDVYSVS S EDRAPFGP ...String: GAMGSRGLWG TRLMEESSTN REKYLKSVLR ELVTYLLFLI VLCILTYGMM SSNVYYYTRM MSQLFLDTPV SKTEKTNFKT LSSMEDFWK FTEGSLLDGL YWKMQPSNQT EADNRSFIFY ENLLLGVPRI RQLRVRNGSC SIPQDLRDEI KECYDVYSVS S EDRAPFGP RNGTAWIYTS EKDLNGSSHW GIIATYSGAG YYLDLSRTRE ETAAQVASLK KNVWLDRGTR ATFIDFSVYN AN INLFCVV RLLVEFPATG GVIPSWQFQP LKLIRYVTTF DFFLAACEII FCFFIFYYVV EEILEIRIHK LHYFRSFWNC LDV VIVVLS VVAIGINIYR TSNVEVLLQF LEDQNTFPNF EHLAYWQIQF NNIAAVTVFF VWIKLFKFIN FNRTMSQLST TMSR CAKDL FGFAIMFFII FLAYAQLAYL VFGTQVDDFS TFQECIFTQF RIILGDINFA EIEEANRVLG PIYFTTFVFF MFFIL LNMF LAIINDTYSE VKSDLAQQKA EMELSD |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II / Details: blot for 7 seconds, -1 mm offset before plunging. | |||||||||
Details | Single particles embedded in lipid nanodiscs. This sample was monodisperse. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1500 / Average exposure time: 0.2 sec. / Average electron dose: 1.35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |